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Table 1 Distribution of SNPs that passed quality control on the chicken genome

From: Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Chromosome

No. SNPs

Physical length (Mb)c

Marker density (kb/SNP)

5% chromosome-wide significance thresholdd

0a

5979

–

–

8.36E-06

1

81,335

195.3

2.40

6.15E-07

2

50,755

148.8

2.93

9.85E-07

3

45,028

110.4

2.45

1.11E-06

4

33,760

90.2

2.67

1.48E-06

5

24,678

59.6

2.41

2.03E-06

6

16,436

35.0

2.13

3.04E-06

7

17,826

36.2

2.03

2.80E-06

8

13,667

28.8

2.10

3.66E-06

9

14,291

23.4

1.64

3.50E-06

10

14,631

19.9

1.36

3.42E-06

11

10,749

19.4

1.80

4.65E-06

12

11,590

19.9

1.72

4.31E-06

13

8589

17.8

2.07

5.82E-06

14

10,062

15.2

1.51

4.97E-06

15

7697

12.7

1.64

6.50E-06

16

273

0.5

1.96

1.83E-04

17

7113

10.5

1.47

7.03E-06

18

7292

11.2

1.54

6.86E-06

19

6517

10.0

1.53

7.67E-06

20

7321

14.3

1.95

6.83E-06

21

6786

6.8

1.00

7.37E-06

22

2877

4.1

1.42

1.74E-05

23

4584

5.7

1.25

1.09E-05

24

5541

6.3

1.14

9.02E-06

25

1860

2.2

1.18

2.69E-05

26

4485

5.3

1.19

1.11E-05

27

3784

5.2

1.38

1.32E-05

28

3862

4.7

1.23

1.29E-05

LGE22C19W28_E50C23b

124

1.0

7.78

4.03E-04

LGE64b

47

0.8

17.02

1.06E-03

Total

429,539

921.2

2.46

1.16E-07

  1. aThese SNPs are not mapped to any chromosome
  2. bTwo linkage groups
  3. cThe physical length of the chromosome was based on the genome build Gallus_gallus-4.0/galGal4 (Nov. 2011)
  4. dBonferroni-corrected 5% chromosome-wise significance threshold = 0.05/number of SNPs after quality control